X-ray vs. NMR structure of N-terminal domain of δ-subunit of RNA polymerase
Language English Country United States Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
24937760
DOI
10.1016/j.jsb.2014.06.001
PII: S1047-8477(14)00137-3
Knihovny.cz E-resources
- Keywords
- N-terminal domain, Nuclear magnetic resonance, Protein crystallography, RNA polymerase, δ-Subunit,
- MeSH
- Bacillus subtilis enzymology MeSH
- DNA-Directed RNA Polymerases chemistry MeSH
- Hydrogen-Ion Concentration MeSH
- Protein Conformation * MeSH
- Crystallography, X-Ray methods MeSH
- Nuclear Magnetic Resonance, Biomolecular methods MeSH
- Protein Structure, Secondary MeSH
- Amino Acid Sequence MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- DNA-Directed RNA Polymerases MeSH
The crystal structure of the N-terminal domain of the RNA polymerase δ subunit (Nδ) from Bacillus subtilis solved at a resolution of 2.0Å is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important β sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Nδ, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni(2+) ions, are the main reason for such a difference. In summary, the study illustrates that the two structural approaches may give unequal results, which need to be interpreted with care to obtain reliable structural information in terms of biological relevance.
References provided by Crossref.org
Triple resonance ¹⁵Ν NMR relaxation experiments for studies of intrinsically disordered proteins
